Rosales sister to Fabales: Towards resolving the rosid puzzle

Molecular Phylogenetics and Evolution

Volumn 44, Issue 1, 2007, Pages 488-493

  Ravi, V ^a   Khurana, Jitendra P ^a   Tyagi, Akhilesh K ^a   Khurana, Paramjit ^a  

^a UNIVERSITY OF DELHI   (India)

Author keywords

[No Author keywords available]

Indexed keywords

VEGETABLE PROTEIN;

ANGIOSPERM; ARTICLE; CLASSIFICATION; GENETICS; LEGUME; NUCLEIC ACID DATABASE; PHYLOGENY; SEQUENCE ALIGNMENT;

DATABASES, NUCLEIC ACID; FABACEAE; PHYLOGENY; PLANT PROTEINS; ROSALES; SEQUENCE ALIGNMENT;

FABALES; MAGNOLIOPHYTA; ROSIDAE;

EID: 34249677317     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2006.11.014     Document Type: Article

References (43)

1. Angiosperm Phylogeny Group (APG), 1998. An ordinal classification for the families of flowering plants. Ann. Missouri Bot. Gard. 85, 531-553.
2. Angiosperm Phylogeny Group (APG II), 2003. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Bot. J. Linn. Soc. 141, 399-436.
3. Asano T., Tsudzuki T., Takahashi S., Shimada H., and Kadowaki K. Complete nucleotide sequence of the sugarcane (Saccharum officinarum) chloroplast genome: a comparative analysis of four monocot chloroplast genomes. DNA Res. 11 (2004) 93-99
4. Cronquist A. An integrated system of classification of flowering plants (1981), Columbia Univ. Press, New York, USA
5. Felsenstein J. PHYLIP - phylogeny inference package (version 3.2). Cladistics 5 (1989) 164-166
6. Goremykin V.V., Hirsch-Ernst K.I., Wolfl S., and Hellwig F.H. The chloroplast genome of the "basal" angiosperm Calycanthus fertilis-structural and phylogenetic analysis. Plant Syst. Evol. 242 (2003) 119-135
7. Goremykin V.V., Hirsch-Ernst K.I., Wolfl S., and Hellwig F.H. Analysis of the Amborella trichopoda chloroplast genome sequence suggests that Amborella is not a basal angiosperm. Mol. Biol. Evol. 20 (2003) 1499-1505
8. Goremykin V.V., Hirsch-Ernst K.I., Wolfl S., and Hellwig F.H. The chloroplast genome of Nymphaea alba: whole-genome analyses and the problem of identifying the most basal angiosperm. Mol. Biol. Evol. 21 (2004) 1445-1454
9. Goremykin V.V., Holland B., Hirsch-Ernst K.I., and Hellwig F.H. Analysis of Acorus calamus chloroplast genome and its phylogenetic implications. Mol. Biol. Evol. 22 (2005) 1813-1822
10. Guindon S., and Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52 (2003) 696-704
11. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids Symp. Ser. 41 (1999) 95-98
12. Hilu K.W., Borsch T., Muller K., Soltis D.E., Soltis P.S., Savolainen V., Chase M., Powell M., Alice L., Evans R., Sauquet H., Neinhuis C., Slotta T., Rohwer J., and Chatrou L. Inference of angiosperm phylogeny based on matK sequence information. Am. J. Bot. 90 (2003) 1758-1776
13. Hupfer H., Swiatek M., Hornung S., Herrmann R.G., Maier R.M., Chiu W.L., and Sears B. Complete nucleotide sequence of the Oenothera elata plastid chromosome, representing plastome I of the five distinguishable euoenothera plastomes. Mol. Gen. Genet. 263 (2000) 581-585
14. Huelsenbeck J.P., and Ronquist F. MRBAYES: bayesian inference of phylogeny. Bioinformatics 17 (2001) 754-755
15. Jansen R.K., Kaittanis C., Saski C., Lee S.B., Tomkins J., Alverson A.J., and Daniell H. Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids. BMC Evol. Biol. 6 (2006) 32
16. Kato T., Kaneko T., Sato S., Nakamura Y., and Tabata S. Complete structure of the chloroplast genome of a legume, Lotus japonicus. DNA Res. 7 (2000) 323-330
17. Keane T.M., Creevey C.J., Pentony M.M., Naughton T.J., and McInerney J.O. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol. Biol. 6 (2006) 29
18. Kim K.J., and Lee H.L. Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Res. 11 (2004) 247-261
19. Lee S.-B., Kaittanis C., Jansen R.K., Hostetler J.B., Tallon L.J., Town C.D., and Daniell H. The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms. BMC Genomics 7 (2006) 61
20. Leebens-Mack J., Raubeson L.A., Cui L., Kuehl J., Fourcade M., Chumley T., Boore J.L., Jansen R.K., and dePamphilis C.W. Identifying the basal angiosperms in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone. Mol. Biol. Evol. 22 (2005) 1948-1963
21. Magallon S., and Sanderson M.J. Relationships among seed plants inferred from highly conserved genes: sorting conflicting phylogenetic signals among ancient lineages. Am. J. Bot. 89 (2002) 1991-2006
22. Manos P.S., and Steele K.P. Phylogenetic analysis of 'higher' Hamamelididae based on plastid sequence data. Am. J. Bot. 84 (1997) 1407-1419
23. Martin W., Deusch O., Stawski N., Grunheit N., and Goremykin V. Chloroplast genome phylogenetics: why we need independent approaches to plant molecular evolution. Trends Plant Sci. 10 (2005) 203-209
24. Page R.D.M. TREEVIEW: an application to display phylogenetic trees on personal computers. Comp. Appl. Biosci. 12 (1996) 357-358
25. Ravi V., Khurana J.P., Tyagi A.K., and Khurana P. The chloroplast genome of mulberry: complete nucleotide sequence, gene organization and comparative analysis. Tree Genet. Genomes 3 (2006) 49-59
26. Saski C., Lee S.-B., Daniell H., Wood T.C., Tomkins J., Kim H.-G., and Jansen R.K. Complete chloroplast genome sequence of Glycine max and comparative analyses with other legume genomes. Plant Mol. Biol. 59 (2005) 309-322
27. Sato S., Nakamura Y., Kaneko T., Asamizu E., and Tabata S. Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Res. 6 (1999) 283-290
28. Savolainen V., Chase M.W., Morton C.M., Soltis D.E., Bayer C., Fay M.F., De Bruijn A., Sullivan S., and Qiu Y.-L. Phylogenetics of flowering plants based upon a combined analysis of plastid atpB and rbcL gene sequences. Syst. Biol. 49 (2000) 306-362
29. Savolainen V., Fay M.F., Albach D.C., Backlund A., Van der bank M., Cameron K.M., Johnson S.A., Lledo M.D., Pintaud J.-C., Powell M., Sheahan M.C., Soltis D.E., Soltis P.S., Weston P., Whitton W.M., Wurdack K.J., and Chase M.W. Phylogeny of the eudicots: a nearly complete familial analysis based on rbcL gene sequences. Kew Bullet. 55 (2000) 257-309
30. Schmitz-Linneweber C., Maier R.M., Alcaraz J.P., Cottet A., Herrmann R.G., and Mache R. The plastid chromosome of spinach (Spinacia oleracea): complete nucleotide sequence and gene organization. Plant Mol. Biol. 45 (2001) 307-315
31. Schmitz-Linneweber C., Regel R., Du T.G., Hupfer H., Herrmann R.G., and Maier R.M. The plastid chromosome of Atropa belladonna and its comparison with that of Nicotiana tabacum: The role of RNA editing in generating divergence in the process of speciation. Mol Biol. Evol. 19 (2002) 1602-1612
32. Shinozaki K., Ohme M., Tanaka M., Wakasugi T., Hayashida N., Matsubayashi T., Zaita N., Chunwongse J., Obokata J., Yamaguchi-Shinozaki K., Ohto C., Torazawa K., Meng B.-Y., Sugita M., Deno H., Kamogashira T., Yamada K., Kusuda J., Takaiwa F., Kato A., Tohdoh N., Shimada H., and Sugiura M. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J. 5 (1986) 2043-2049
33. Soltis D.E., Albert V.A., Savolainen V., Hilu K., Qiu Y.L., Chase M.W., Farris J.S., Stefanovic S., Rice D.W., Palmer J.D., and Soltis P.S. Genome-scale data, angiosperm relationships, and 'ending incongruence': a cautionary tale in phylogenetics. Trends Plant Sci. 9 (2004) 477-483
34. Soltis D.E., Senters A.E., Zanis M., Kim S., Thompson J.D., Soltis P.S., Ronse De Craene L.P., Endress P.K., and Farris J.S. Gunnerales are sister to other core eudicots: implications for the evolution of pentamery. Am. J. Bot. 90 (2003) 461-470
35. Soltis D.E., Soltis P.S., Chase M.W., Mort M.E., Albach D.C., Zanis M., Savolainen V., Hahn W.J., Hoot S.B., Fay M.F., Axtell M., Swensen S.M., Prince L.M., Kress W.J., Nixon K.C., and Farris J.S. Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences. Bot. J. Linn. Soc. 133 (2000) 381-461
36. Soltis D.E., Soltis P.S., Morgan D.R., Swensen S.M., Mullin B.C., Dowd J.M., and Martin P.G. Chloroplast gene sequence data suggest a single origin of the predisposition for symbiotic nitrogen fixation in angiosperms. Proc. Natl. Acad. Sci. USA 92 (1995) 2647-2651
37. Soltis P.S., and Soltis D.E. The origin and diversification of angiosperms. Am. J. Bot. 91 (2004) 1614-1626
38. Steane D.A. Complete nucleotide sequence of the chloroplast genome from the Tasmanian blue gum, Eucalyptus globulus (Myrtaceae). DNA Res. 12 (2005) 215-220
39. Stefanovic S., Rice D.W., and Palmer J.D. Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots?. BMC Evol. Biol. 4 (2004) 35
40. Sytsma K.J., Morawetz J., Pires J.C., Nepokroeff M., Conti E., Zjhra M., Hall J.C., and Chase M.W. Urticalean rosids: circumscription, rosid ancestry, and phylogenetics based on rbcL, trnL-F, and ndhF sequences. Am. J. Bot. 89 (2002) 1531-1546
41. Takhtajan A. Outline of the classification of flowering plants (Magnoliophyta). Bot. Rev. 46 (1980) 225-359
42. Takhtajan A. Diversification and classification of flowering plants (1997), Columbia Univ. Press, New York, USA
43. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680